When yeast is recovered from a fermenter with the intention of re-using the yeast for a subsequent fermentation it is referred to as cropping of the yeast. The timing of the cropping is important to recover yeast with maximum nutritional reserves.

It is inevitable that yeast will need to be stored between cropping and pitching. By keeping the yeast cold the yeast metabolism is slowed down so that nutritional reserves are available so that the yeast doesn't starve during storage.

Primary fermentation takes place in a bucket or carboy, sometimes left open but often stoppered with the carbon dioxide gas produced venting through a fermentation lock. During this time, temperatures should be kept at optimum temperature for the fermentation process. For ale this temperature is usually 65-75°F / 18-24°C, and for lager it is usually much colder, around 50°F / 10°C. Starting within 12 hours and continuing over the next few days a vigorous fermentation takes place. During this stage the simple sugar maltose in the wort is consumed by the yeast. A layer of sediment, the trub, appears at the bottom of the fermenter, composed of heavy fats, proteins and inactive yeast. A sure sign that primary fermentation has finished is that the head of foam (krausen), built by bubbling of CO2, falls.

Often, the beer is then siphoned into another container, usually a carboy, for aging or secondary fermentation. The siphoning is done to separate the batch from the afore-mentioned layer of sediment so that it is not used as food, as this can give the beer a off-flavor. During secondary fermentation the heavier, more complex sugars and impurities are digested. Secondary fermentation can take from 2 to 4 weeks, sometimes longer, depending on the type of beer. Some homebrewers will keep the batch in the primary fermenter (called single stage fermentation) for secondary fermentation and simply put up with any off flavors. This eliminates the need for a second container, reduces labor, and reduces the likelihood of contaminating the batch with bacteria, or oxidizing it, during transfer to the second container. This is a good beginner strategy, especially for those not skilled with siphoning liquids.